8
votes
relation between Illumina sequencing primer and viral sequences
You'll unfortunately find adapter sequences contaminating a lot of entries in Genbank. In short, the sequence is most likely either an unassembled fragment where the input into the assembly step hadn'...
- 19.8k
6
votes
What is the origin of HIV1?
They are both lentiviruses and share a distant common ancestor.
HIV-1 and HIV-2 are descendents from simian immunodeficiency virus (SIV). The following tree shows the relationships very clearly, from ...
M__♦
- 13k
5
votes
Accepted
How to get the number of complete phage genomes available on ncbi?
Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore
Copy and paste the search term:
...
M__♦
- 13k
4
votes
Accepted
Genome assembly of SRR12196449 with SPAdes
Update 2:
I looked into this a little more, with the various data sources.
This is related in part to the answer submitted by OP juanjo75es, in addition to discussion on chat. I don't entirely ...
- 4,252
4
votes
Accepted
How to sort multiple FASTA files based on their content?
The general idea is:
iterate over all files
read the first line of each file, extract the segment bit
move the file based on that
In Python, this can be done in ...
- 4,895
3
votes
Label protein strucuture residues in Chimera
You cant do this in Chimera, but in pymol you can write a script to do this.
In terms of the view, you can use get_view on the command line. This returns a section that you can copy and paste in - ...
- 41
2
votes
RNA-seq analysis of mixed viral/host reads with salmon
You provide Salmon with a transcriptome fasta... so merging the human transcriptome with the pox virus genome fasta file should work. You don't mention that in your post but the viral genome should ...
- 1,613
2
votes
Genome assembly of SRR12196449 with SPAdes
After many considerations, I am going to accept the response from Maximilian Press. I see now that some viruses have high variability (HIV even 50% of the sequence). Therefore MN630242.1. and U11820.1 ...
- 359
2
votes
Accepted
Using sickle for quality trimming
It'd be rare to run into Illumina encoded quality scores any more, I doubt there are machines running that still produce those. Everything produced at the moment uses Sanger encoded (phred + 33) ...
- 19.8k
2
votes
Accepted
Demovir produces an empty output
maybe you can open the demovir.R file with Rstudio and execute line by line to check where the failure is. - @zorbax
Thanks for your suggestion. I eventually got a correct final output already.
The ...
- 41
2
votes
Accepted
Entrez (Biopython) esearch and efetch not returning sequence as expected
Did you try to fetch from the database nucleotide instead of gene ?
...
2
votes
Accepted
Align the HIV-1 Gag protein with the Gag protein of Visna virus
Both are lentiviruses and env is a fast evolving gene. What you are looking at here is the location of indels and this will vary between alignment algorithms.
There ...
M__♦
- 13k
2
votes
How to get the number of complete phage genomes available on ncbi?
How about trying this?
Go to https://www.ncbi.nlm.nih.gov/nucleotide. Then type the following command in the search box. It resulted in 23971 items.
...
- 636
1
vote
What is the limit of partition incompleteness in Bayesian MCMC?
The original answer was "criticised" for being obtuse.
The basic very simple answer is:
If the data you present in the diagram (alignment) is left EXACTLY in the format used to make the ...
M__♦
- 13k
1
vote
How to sort multiple FASTA files based on their content?
The general idea is:
iterate over all files
read the first line of each file, extract the segment bit
move the file based on that
In Python, this can be done in ...
- 4,895
1
vote
Accepted
Is current AI able to generate RNA sequences of viruses?
Reinforced learning is an interesting technology, but they are prone to extreme results - which are not necessarily at all biological feasible. Google can use it to outperform, or very possibly ...
M__♦
- 13k
1
vote
Accepted
Metagenomics pipeline recommendations for short-read data
Under my experience, the best ones in completeness and N50 are s-aligner, Megahit and rnaSPAdes, but I admit I didn't test the other ones for different reasons. Broad indeed seems to use internally ...
- 359
1
vote
Accepted
How to use GEO_SPHERE?
As it is turned out from the author's words:
This is a normal result for the tutorial.
It is recommended to border the deviation of geomodel to 3 powers.
There is set up a homogenous diffusion model ...
- 435
1
vote
Gold standard benchmark
Thanks for raising the issue, it is certainly topical. The question is whether the data set they unit tested is reliable.
I think the issue they are trying get to is mosaic artefacts in the sequencing ...
M__♦
- 13k
1
vote
Accepted
Gold standard benchmark
Anyone can declare anything to be a "gold-standard", the term is meaningless. All if actually means is, "we think this is the test that everything else should be benchmarked against&...
- 19.8k
1
vote
How to sort multiple FASTA files based on their content?
One "out there" approach you could take is to create a fasta file containing your regions of interest (as separate sequences), and then map your fasta files to that reference fasta file, ...
- 15.1k
1
vote
What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?
My recollection of a conversation I had with Justin O'Grady is that it's about 99% host DNA for unfiltered samples. There are a few ways to reduce that portion prior to sequencing. He has written a ...
- 15.1k
1
vote
Accepted
How to create a nexus file for BEAST?
Its easy,
Download the data from NCBI in fasta format (its an option in one of the pull down headers).
Load it into the latest version of MEGA, version 7(?), perform the alignment therein.
Export ...
M__♦
- 13k
1
vote
Resources to learn genome assembly workflow for small genomes (like viruses)
I would recommend a specific tool for viral meta genomics rather than using applying a general tool into a specific technical challenge. Here are the ones discussed on Bioinfo SE for de novo ...
M__♦
- 13k
1
vote
How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?
I found a possible answer to my own question by reading this biostar page and also finding an NCBI page for downloading the reference genome file for viruses.
You should go to this NCBI page and ...
- 169
1
vote
How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?
You might be interested in the viral sequence data from CATCH. There are various different viral subsets available.
You could also try the NCBI virus website, filtering on human hosts. There's a "...
- 15.1k
1
vote
How to calculate mutation rate and mutation sites in a genome using FASTA file?
You can still align a FASTA file with a tool like bwa mem ( if they are short reads ) or minimap2 for long reads and run it through a variant caller like freebayes. Alternatively, if you have ...
1
vote
Annotation with Prokka or RAST
If you are looking for another tool, you could try eggnog mapper: it is an annotation tool based on orthology assignments. The EggNOG database happens to have a section for viral Orthologous Groups so ...
1
vote
Annotation with Prokka or RAST
I was able to get good annotation using prokka by using following commands in prokka.
...
- 719
Only top scored, non community-wiki answers of a minimum length are eligible